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- PDB-6e9b: Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL)... -

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Basic information

Entry
Database: PDB / ID: 6e9b
TitleBacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-B in complex with mixed-linkage heptasaccharide
ComponentsMixed-linkage glucan utilization locus (MLGUL) SGBP-B
KeywordsSUGAR BINDING PROTEIN / tetratricopeptide repeat / outer membrane protein / binding protein
Function / homologyImmunoglobulin-like fold / PKD domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsTamura, K. / Gardill, B.R. / Brumer, H. / Van Petegem, F.
CitationJournal: Cell.Mol.Life Sci. / Year: 2019
Title: Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus.
Authors: Tamura, K. / Foley, M.H. / Gardill, B.R. / Dejean, G. / Schnizlein, M. / Bahr, C.M.E. / Louise Creagh, A. / van Petegem, F. / Koropatkin, N.M. / Brumer, H.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
B: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
C: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
D: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,82715
Polymers182,7134
Non-polymers2,11411
Water1,20767
1
A: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0635
Polymers45,6781
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8703
Polymers45,6781
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8703
Polymers45,6781
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mixed-linkage glucan utilization locus (MLGUL) SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0234
Polymers45,6781
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.292, 242.207, 75.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Mixed-linkage glucan utilization locus (MLGUL) SGBP-B


Mass: 45678.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02744 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7LY28
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1b_1-5]/1-1-1-1-1-1-1/a3-b1_b4-c1_c4-d1_d4-e1_e3-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 71.59 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2M lithium sulfate, 0.1M phosphate-citrate, 20% (w/v) PEG1000
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 50094 / % possible obs: 99.8 % / Redundancy: 7.42 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 3.15→3.34 Å / Redundancy: 7.44 % / Mean I/σ(I) obs: 1.73 / Num. unique obs: 7894 / CC1/2: 0.651 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Cootmodel building
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+57 / Resolution: 3.15→34.33 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 1.087 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.02 / SU Rfree Blow DPI: 0.398 / SU Rfree Cruickshank DPI: 0.407
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2505 5 %RANDOM
Rwork0.221 ---
obs0.224 50093 100 %-
Displacement parametersBiso max: 207.63 Å2 / Biso mean: 100.53 Å2 / Biso min: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1-10.5401 Å20 Å20 Å2
2---7.0024 Å20 Å2
3----3.5377 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: final / Resolution: 3.15→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11168 0 128 67 11363
Biso mean--103.99 59.23 -
Num. residues----1514
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3706SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1983HARMONIC5
X-RAY DIFFRACTIONt_it11486HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1673SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12882SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11486HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15726HARMONIC21.32
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion23.63
LS refinement shellResolution: 3.15→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3271 50 4.99 %
Rwork0.2721 952 -
all0.2748 1002 -
obs--99.3 %

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